Investigations
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The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant Arabidopsis thaliana. The work will be published as Urquiza-Garcia, Molina, Halliday and Millar, title "Abundant clock proteins point to missing molecular regulation in the plant circadian clock", in Molecular Systems Biology, 2025.
Starting from the U2019.3 and U2020.3 models, this project rescales parameters to match protein levels that were predicted using a simple model from the TiMet ...
Submitter: Andrew Millar
Studies: Construction of NanoLUC-tagged plants, Estimating DNA-binding affinities for Arabidopsis proteins, Measuring absolute levels of clock proteins with calibrated NanoLUC assays, Predicting absolute levels of clock proteins with a simple model, Recalibrating the clock models for absolute protein levels, to create mo..., Reproducibility documentation
Assays: Clock protein number determination with NanoLUC calibration, Clock proteins NanoLUC fusion raw data, Gatway maps of genomic regions of clock genes, In vivo bioluminescence of clock protein-NanoLUC fusions: example experi..., Jupyter notebook Predicting Protein Numbers, Propagating scaling factors into model parameters for U2019.4->U2019.5 a..., Protein level time series, Python packages, Reproducibility tool set, Selection of complemented transgenic lines, TiMet RNA timeseries data, promoter binding affinity calculations on the genome based on PBMs and E...
Data, FMv2 model and simulations for the Chew et al. 2017 paper (bioRxiv https://doi.org/10.1101/105437 ), updated in 2022, mostly on the prr7 prr9 double mutant, with controls in lsf1 and prr7 single mutants. This is one of the outputs from the EU FP7 TiMet project, https://fairdomhub.org/projects/92.
This data archive was updated during submisson to the journal _in Silico _Plants in 2022, and a Snapshot was published. The updates are not changing the core data or the FMv2 model that has been ...
Submitter: Andrew Millar
Studies: Analysis of Framework Model version 2 (FMv2), Construction of Framework Model version 2 (FMv2), Test of FMv2, follow-on: mechanisms of malate/fumarate accumulation, Test of FMv2, photoperiodic flowering and hypocotyl elongation, Test of FMv2, study Gibberellins 1, Test of FMv2, study Laurel & Hardy 1, Test of FMv2, study Laurel & Hardy 2, Test of FMv2, study Laurel & Hardy 3, Tests of FMv2, compilations and figures
Assays: Assimilation and partitioning of 14CO2 at night, Biomass and metabolites, Biomass and metabolites, Biomass and metabolites, Biomass, leaf area and gas exchange data, Biomass, leaf number and metabolites, Circadian period analysis, Composition of FMv2, FMv2 simulation, FMv2 simulation, FMv2 simulation, Mizuno lab, Flowering time in clock mutants, Mizuno lab, Hypocotyl length in clock mutants, Relationship among FMv2 outputs, Sensitivity analysis of FMv2, Simulating clock gene expression with model P2011.1.2, Thiamine vitamers, TiMet WP1.1, Clock gene expression in clock mutants, TiMet WP1.1a Metabolite analysis of clock mutants
The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant Arabidopsis thaliana. The work is published in Urquiza-Garcia and Millar, Testing the inferred transcription rates of a dynamic, gene network model in absolute units, In Silico Plants, 2021.
Starting from the P2011 model, this project corrects theoretical issues (EC steady state binding assumption) to form an intermediate model (first version U2017.1; published as U2019.1) model, rescales ...
Collection of models submitted to PLaSMo by Uriel Urquiza Garcia and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: F2014.1 - PLM_1030, PLM_67v3withTempPulse - PLM_81
Assays: F2014.1 - PLM_1030, version 1, PLM_67v3withTempPulse - PLM_81, version 1
Project to test effects of temperature cycles on expression of Arabidopsis florigen gene FT, and whether these are mediated by temperature-dependent leaf development or temperature-specific FT expression, or both. Re-used and extended Arabidopsis Framework Model v1 to address this question. Led by Hannah Kinmonth-Schultz in Kim and Imaizumi labs, collaborating with Millar lab.
Submitter: Andrew Millar
Collection of models submitted to PLaSMo by Yin Hoon and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Chew_et_al_2012_Photothermal_Model - PLM_73, Chew_et_al_2014_Framework_Model - PLM_76, Part_of_Christophe_et_al_2008_Functional_Structural_Plant_Model - PLM_75, Salazar Photoperiodism Model with T6P - PLM_82, Salazar_et_al_2009_Photoperiodism_Model - PLM_74
Assays: Chew_et_al_2012_Photothermal_Model - PLM_73, version 1, Chew_et_al_2014_Framework_Model - PLM_76, version 1, Part_of_Christophe_et_al_2008_Functional_Structural_Plant_Model - PLM_75..., Salazar Photoperiodism Model with T6P - PLM_82, version 1, Salazar_et_al_2009_Photoperiodism_Model - PLM_74, version 1
Collection of models submitted to PLaSMo by Andrew Millar and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Arabidopsis clock model P2011, graphical diagram - PLM_1045, Arabidopsis clock model P2011.3.1 - PLM_1041, Arabidopsis clock model P2011.4.1 - PLM_1042, Arabidopsis clock model P2011.5.1 - PLM_1043, Arabidopsis clock model P2011.6.1 - PLM_1044, Arabidopsis clock models P2011.1.2 and P2011.2.1 - PLM_71, Arabidopsis_clock_P2011 - PLM_64, Arabidopsis_clock_P2012 - PLM_70, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, At_Pokh2011v6_plasmo_ltdParams.xml - PLM_68, AuxSim - PLM_27, AuxSim full - PLM_30, DomijanTS_AtClock2011 - PLM_50, Locke2005_CircadianClock_tanh - PLM_8, Locke2006_CircadianClock_tanh - PLM_10, OK MEP pathway 2013 - PLM_72, P2012_AJMv2_NoABA - PLM_69, Salazar2009_FloweringPhotoperiod - PLM_9, Sorokina2011_Ostreo_starch - PLM_44, Wilczek photothermal Science - PLM_48
Assays: Arabidopsis clock model P2011, graphical diagram - PLM_1045, version 1, Arabidopsis clock model P2011.1.2 - PLM_71, version 1, Arabidopsis clock model P2011.2.1 - PLM_71, version 2, Arabidopsis clock model P2011.3.1 - PLM_1041, version 1, Arabidopsis clock model P2011.4.1 - PLM_1042, version 1, Arabidopsis clock model P2011.5.1 - PLM_1043, version 1, Arabidopsis clock model P2011.6.1 - PLM_1044, version 1, Arabidopsis_clock_P2011 - PLM_64, version 1, Arabidopsis_clock_P2011 - PLM_64, version 2, Arabidopsis_clock_P2011 - PLM_64, version 3, Arabidopsis_clock_P2011 - PLM_64, version 4, Arabidopsis_clock_P2012 - PLM_70, version 1, Arabidopsis_clock_P2012 - PLM_70, version 2, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 1, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 2, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 3, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 4, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 5, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 6, At_Pokh2011v6_plasmo_ltdParams.xml - PLM_68, version 1, AuxSim - PLM_27, version 1, AuxSim full - PLM_30, version 1, DomijanTS_AtClock2011 - PLM_50, version 1, DomijanTS_AtClock2011 - PLM_50, version 2, Locke2005_CircadianClock_tanh - PLM_8, version 1, Locke2006_CircadianClock_tanh - PLM_10, version 1, OK MEP pathway 2013 - PLM_72, version 1, P2012_AJMv2_NoABA - PLM_69, version 1, P2012_AJMv2_NoABA - PLM_69, version 2, Salazar2009_FloweringPhotoperiod - PLM_9, version 1, Salazar2009_FloweringPhotoperiod - PLM_9, version 2, Sorokina2011_Ostreo_starch - PLM_44, version 1, Wilczek photothermal Science - PLM_48, version 1, Wilczek photothermal Science - PLM_48, version 2
Project to test effects of natural compared to growth chamber 16:8 LD cycles, on expression of Arabidopsis flowering-time genes, and to define the genetic mechanisms and environmental triggers involved. Led by Young-Hun Song and Akane Kubota in the Imaizumi lab, with collaborators testing plants in parallel in Zurich and Edinburgh.
Collection of models submitted to PLaSMo by Tomasz Zielinski and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Checking upload for andrew - PLM_1040, Plasmo test model1 - PLM_80
Assays: CHecking if all works - PLM_1000, version 111, Checking upload for andrew - PLM_1040, version 1, Plasmo test model1 - PLM_80, version 1, Test created 1552502361596, Test created 1552502791700, Test created 1552503965203, Test created 1552503978484, Test created 1552504117107, Test created 1552504664537, Test created 1552504857803, Test created 1552505193451
Collection of models submitted to PLaSMo by Alexandra Graf and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: TiMet 2011 PP interaction network - PLM_56, TiMet 2011 Pollen network - PLM_54, TiMet 2011 Root network - PLM_55, TiMet 2011 flower specific protein detection network - PLM_57, TiMet 2011 seed network - PLM_53, TiMet 2011 shoot specific diurnal transcript oscillation network - PLM_58, TiMet 2011 silqueue specific protein detection network - PLM_59
Assays: TiMet 2011 PP interaction network - PLM_56, version 1, TiMet 2011 Pollen network - PLM_54, version 1, TiMet 2011 Pollen network - PLM_54, version 2, TiMet 2011 Root network - PLM_55, version 1, TiMet 2011 flower specific protein detection network - PLM_57, version 1, TiMet 2011 seed network - PLM_53, version 1, TiMet 2011 seed network - PLM_53, version 2, TiMet 2011 shoot specific diurnal transcript oscillation network - PLM_5..., TiMet 2011 silqueue specific protein detection network - PLM_59, version 1
Collection of models submitted to PLaSMo by Carl Troein and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: T2011 Ostreococcus clock, CCA1 degr D - PLM_86, T2011 Ostreococcus clock, CCA1 degr L - PLM_85, T2011 Ostreococcus clock, CCA1 prod D - PLM_88, T2011 Ostreococcus clock, CCA1 prod L - PLM_87, T2011 Ostreococcus clock, TOC1 act D - PLM_92, T2011 Ostreococcus clock, TOC1 act L - PLM_91, T2011 Ostreococcus clock, TOC1 degr D - PLM_90, T2011 Ostreococcus clock, TOC1 degr L - PLM_89, T2011 Ostreococcus clock, acc immediate - PLM_83, T2011 Ostreococcus clock, acc on - PLM_84, Troein Ostreococcus clock 1-loop - PLM_7
Assays: T2011 Ostreococcus clock, CCA1 degr D - PLM_86, version 1, T2011 Ostreococcus clock, CCA1 degr L - PLM_85, version 1, T2011 Ostreococcus clock, CCA1 prod D - PLM_88, version 1, T2011 Ostreococcus clock, CCA1 prod L - PLM_87, version 1, T2011 Ostreococcus clock, TOC1 act D - PLM_92, version 1, T2011 Ostreococcus clock, TOC1 act L - PLM_91, version 1, T2011 Ostreococcus clock, TOC1 degr D - PLM_90, version 1, T2011 Ostreococcus clock, TOC1 degr L - PLM_89, version 1, T2011 Ostreococcus clock, TOC1 degr L - PLM_89, version 2, T2011 Ostreococcus clock, acc immediate - PLM_83, version 1, T2011 Ostreococcus clock, acc on - PLM_84, version 1, Troein Ostreococcus clock 1-loop - PLM_7, version 1, Troein Ostreococcus clock 1-loop - PLM_7, version 2
Collection of models submitted to PLaSMo by Richard Adams and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Modified Locke Arabadopsis 3 loop Circadian Clock - PLM_66, Neurospora Circadian Clock 3-variable model - PLM_51, Neurospora Circadian Clock 3-variable model - sinusoidal light oscillati...
Assays: Modified Locke Arabadopsis 3 loop Circadian Clock - PLM_66, version 1, Neurospora Circadian Clock 3-variable model - PLM_51, version 1, Neurospora Circadian Clock 3-variable model - sinusoidal light oscillati...
Collection of models submitted to PLaSMo by Jonathan Massheder and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: LINTUL_V2 - PLM_42, SUCROS1 - PLM_24
Assays: LINTUL_V2 - PLM_42, version 1, SUCROS1 - PLM_24, version 1
Collection of models submitted to PLaSMo by Rob Smith and automatically transferred to FAIRDOM Hub.
Collection of models submitted to PLaSMo by Martin Beaton and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Central plant metabolism - PLM_61, Glycolysis SBGN - PLM_60, Insulin-like growth factor signaling - PLM_62, Martin test - PLM_65, Neuronal muscle signalling - PLM_63
Assays: Central plant metabolism - PLM_61, version 1, Glycolysis SBGN - PLM_60, version 1, Insulin-like growth factor signaling - PLM_62, version 1, Martin test - PLM_65, version 1, Martin test - PLM_65, version 2, Neuronal muscle signalling - PLM_63, version 1
Collection of models submitted to PLaSMo by Maria-Luisa Guerriero and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: arabidopsis_clock_biopepa - PLM_47
Collection of models submitted to PLaSMo by Alexandra Pokhilko and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Arabidopsis_clock_2011 - PLM_43, Arabidopsis_clock_2012_TOC1_repressor - PLM_49, Arabidopsis_clock_extend - PLM_6
Assays: Arabidopsis_clock_2011 - PLM_43, version 1, Arabidopsis_clock_2011 - PLM_43, version 2, Arabidopsis_clock_2011 - PLM_43, version 3, Arabidopsis_clock_2011 - PLM_43, version 4, Arabidopsis_clock_2011 - PLM_43, version 5, Arabidopsis_clock_2011 - PLM_43, version 6, Arabidopsis_clock_2011 - PLM_43, version 7, Arabidopsis_clock_2011 - PLM_43, version 8, Arabidopsis_clock_2011 - PLM_43, version 9, Arabidopsis_clock_2012_TOC1_repressor - PLM_49, version 1, Arabidopsis_clock_2012_TOC1_repressor - PLM_49, version 2, Arabidopsis_clock_extend - PLM_6, version 1, Arabidopsis_clock_extend - PLM_6, version 2, Arabidopsis_clock_extend - PLM_6, version 3
Collection of models submitted to PLaSMo by Daniel Seaton and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Arabidopsis - starch and the circadian clock, Model 1 (Seaton et al., 20..., Arabidopsis - starch and the circadian clock, Model 2 (Seaton et al., 20..., Arabidopsis - starch and the circadian clock, Model 3 (Seaton et al., 20..., Modelling circadian regulation of flowering time and hypocotyl elongatio...
Assays: Arabidopsis - starch and the circadian clock, Model 1 (Seaton et al., 20..., Arabidopsis - starch and the circadian clock, Model 2 (Seaton et al., 20..., Arabidopsis - starch and the circadian clock, Model 3 (Seaton et al., 20..., Modelling circadian regulation of flowering time and hypocotyl elongatio...
Collection of models submitted to PLaSMo by Chris Davey and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: AFRC Wheat 2 evapw submodel - PLM_33, AFRC Wheat 2 jdaydif submodel - PLM_34, AFRC Wheat 2 julday submodel - PLM_35, AFRC Wheat 2 ldim submodel - PLM_36, AFRC Wheat 2 photpd submodel - PLM_37, AFRC Wheat 2 tdays submodel - PLM_38, AFRC Wheat 2 vappres submodel - PLM_39, AFRC Wheat 2 vernal submodel - PLM_40, AFRC Wheat 2 weathr submodel - PLM_41, AFRC Wheat2 dev submodel - PLM_32, AFRCtest2 - PLM_25, Arabidopsis leaf carbohydrate model (Rasse and Tocquin) - PLM_2, C3 photosynthesis (Farquhar, von Caemmerer, Berry) model - PLM_1, Miscanmod - PLM_3
Assays: AFRC Wheat 2 evapw submodel - PLM_33, version 1, AFRC Wheat 2 jdaydif submodel - PLM_34, version 1, AFRC Wheat 2 julday submodel - PLM_35, version 1, AFRC Wheat 2 ldim submodel - PLM_36, version 1, AFRC Wheat 2 photpd submodel - PLM_37, version 1, AFRC Wheat 2 tdays submodel - PLM_38, version 1, AFRC Wheat 2 vappres submodel - PLM_39, version 1, AFRC Wheat 2 vernal submodel - PLM_40, version 1, AFRC Wheat 2 weathr submodel - PLM_41, version 1, AFRC Wheat2 dev submodel - PLM_32, version 1, AFRCtest2 - PLM_25, version 1, Arabidopsis leaf carbohydrate model (Rasse and Tocquin) - PLM_2, version 1, C3 photosynthesis (Farquhar, von Caemmerer, Berry) model - PLM_1, version 1, Miscanmod - PLM_3, version 1
Collection of models submitted to PLaSMo by Robert Muetzelfeldt and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: 3PG - PLM_12, CENTURY_Rowe_daily - PLM_22, DALEC - PLM_23, LINTUL - PLM_4, McMurtrie vegetation model - PLM_11, TRIFFID - PLM_5
Assays: 3PG - PLM_12, version 1, CENTURY_Rowe_daily - PLM_22, version 1, DALEC - PLM_23, version 1, LINTUL - PLM_4, version 1, McMurtrie vegetation model - PLM_11, version 1, McMurtrie vegetation model - PLM_11, version 2, TRIFFID - PLM_5, version 1
Click on Snapshot 2 to download data, models and analysis for Daniel Seaton et al. biorXiv 2017 https://doi.org/10.1101/182071 and Molecular Systems Biology, accepted Jan 2018, https://doi.org/10.15252/msb.20177962. Note that the published paper cannot be fully linked into this record as the DOI above was not live when we made the Research Object from this Investigation on FAIRDOMHub.
Submitter: Andrew Millar
Studies: Modelling and analysis of translational coincidence, Photoperiod-specific proteome data for Arabidopsis, Proteome and translation rate data for the Ostreococcus alga and for cya..., Rhythmic and photoperiod-specific transcriptome datasets for Arabidopsis
Assays: Aryal et al, 2011, metabolic labelling of Cyanothece protein synthesis, Blasing et al, 2005, diurnal microarray in 12L:12D, Estimation of rates of translation and turnover from proteomics datasets, Martin et al, 2012, Ostreococcus N15 labelling proteomics data, Photoperiod proteomics, Stitt lab, TiMet photoperiod microarrays, Translational coincidence model
Data, models and simulations for the Chew et al. 2014 paper (PNAS, https://doi.org/10.1073/pnas.1410238111), using wild-type Arabidopsis ecotype Col-0 in standard 12hL:12hD growth conditions, compared to La(er) or Fei-0 accessions, or to plants overexpressing a micro RNA (miR156).
Submitter: Andrew Millar
Studies: Construction of Framework Model v1, Test of FMv1, growth study of Col-0 accession in 12L:12D, Test of FMv1, growth study of Col-0 accession in 5 photoperiods, Test of FMv1, growth study of other accessions and transgenic line in 12...
Assays: Arabidopsis Framework Model v1, Matlab and Simile version, Gas exchange of Fei-0 and Ler plants in 12hL:12hD, Growth of Col-0 and 35S:miR156 plants in 12hL:12hD, Growth of Col-0 in 12hL:12hD, Growth of Col-0 plants in 5 photoperiods, Growth of Fei-0 and Ler plants in 12hL:12hD
